HEADER DNA BINDING PROTEIN/DNA 28-MAY-18 5ZYU TITLE THE CRYSTAL STRUCTURE OF HUMANMGME1 WITH SINGLE STRAND DNA2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*CP*AP*AP*CP*AP*AP*CP*A)-3'); COMPND 3 CHAIN: E, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: MITOCHONDRIAL GENOME MAINTENANCE EXONUCLEASE 1; COMPND 7 CHAIN: A, B; COMPND 8 EC: 3.1.-.-; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 GENE: MGME1, C20ORF72, DDK1; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS HUAMNMGME1, DNA COMPLEX, DNA EXONUCLEASE, DNA BINDING PROTEIN, DNA KEYWDS 2 BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.YANG,J.GAN REVDAT 6 22-NOV-23 5ZYU 1 REMARK REVDAT 5 28-AUG-19 5ZYU 1 TITLE SOURCE REVDAT 4 23-JAN-19 5ZYU 1 TITLE REVDAT 3 28-NOV-18 5ZYU 1 JRNL REVDAT 2 31-OCT-18 5ZYU 1 JRNL REVDAT 1 19-SEP-18 5ZYU 0 JRNL AUTH C.YANG,R.WU,H.LIU,Y.CHEN,Y.GAO,X.CHEN,Y.LI,J.MA,J.LI,J.GAN JRNL TITL STRUCTURAL INSIGHTS INTO DNA DEGRADATION BY HUMAN JRNL TITL 2 MITOCHONDRIAL NUCLEASE MGME1 JRNL REF NUCLEIC ACIDS RES. V. 46 11075 2018 JRNL REFN ESSN 1362-4962 JRNL PMID 30247721 JRNL DOI 10.1093/NAR/GKY855 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.050 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 55877 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.210 REMARK 3 FREE R VALUE TEST SET COUNT : 2912 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 28.3719 - 4.8263 1.00 2635 142 0.1777 0.1862 REMARK 3 2 4.8263 - 3.8338 1.00 2620 157 0.1416 0.1562 REMARK 3 3 3.8338 - 3.3500 1.00 2627 138 0.1502 0.1888 REMARK 3 4 3.3500 - 3.0441 1.00 2634 163 0.1673 0.1942 REMARK 3 5 3.0441 - 2.8262 1.00 2618 174 0.1774 0.1858 REMARK 3 6 2.8262 - 2.6597 1.00 2629 158 0.1779 0.2308 REMARK 3 7 2.6597 - 2.5266 1.00 2582 168 0.1748 0.2282 REMARK 3 8 2.5266 - 2.4166 1.00 2665 124 0.1772 0.1762 REMARK 3 9 2.4166 - 2.3236 1.00 2615 160 0.1685 0.2163 REMARK 3 10 2.3236 - 2.2435 1.00 2685 128 0.1644 0.2037 REMARK 3 11 2.2435 - 2.1734 1.00 2593 178 0.1703 0.2017 REMARK 3 12 2.1734 - 2.1113 1.00 2652 134 0.1707 0.1952 REMARK 3 13 2.1113 - 2.0557 1.00 2607 154 0.1772 0.2161 REMARK 3 14 2.0557 - 2.0056 1.00 2674 130 0.1890 0.2122 REMARK 3 15 2.0056 - 1.9600 1.00 2629 126 0.1857 0.2083 REMARK 3 16 1.9600 - 1.9183 1.00 2633 130 0.2069 0.2516 REMARK 3 17 1.9183 - 1.8799 1.00 2684 140 0.2104 0.2381 REMARK 3 18 1.8799 - 1.8444 0.99 2636 120 0.2199 0.2601 REMARK 3 19 1.8444 - 1.8115 0.91 2393 112 0.2368 0.2868 REMARK 3 20 1.8115 - 1.7808 0.73 1952 101 0.2456 0.2981 REMARK 3 21 1.7808 - 1.7521 0.47 1202 75 0.2760 0.2810 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 3955 REMARK 3 ANGLE : 1.036 5421 REMARK 3 CHIRALITY : 0.067 607 REMARK 3 PLANARITY : 0.006 638 REMARK 3 DIHEDRAL : 18.631 2310 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -66.4902 21.7835 -68.6166 REMARK 3 T TENSOR REMARK 3 T11: 0.0743 T22: 0.1130 REMARK 3 T33: 0.1321 T12: -0.0305 REMARK 3 T13: 0.0058 T23: 0.0028 REMARK 3 L TENSOR REMARK 3 L11: 0.4436 L22: 0.3324 REMARK 3 L33: 0.5332 L12: 0.1123 REMARK 3 L13: 0.3694 L23: 0.2074 REMARK 3 S TENSOR REMARK 3 S11: -0.0435 S12: -0.0187 S13: 0.1250 REMARK 3 S21: -0.0201 S22: -0.0204 S23: 0.0741 REMARK 3 S31: -0.0542 S32: -0.0374 S33: 0.0567 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5ZYU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1300007880. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58405 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5ZYT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M PHOSPHORIC-CITRIC ACID PH 4.2 REMARK 280 AND 20% PEG300, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.17933 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.58967 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 DA E 1 REMARK 465 DA E 2 REMARK 465 DA E 11 REMARK 465 DC E 12 REMARK 465 DA E 13 REMARK 465 DA E 14 REMARK 465 DC E 15 REMARK 465 DA C 1 REMARK 465 DA C 2 REMARK 465 DA C 11 REMARK 465 DC C 12 REMARK 465 DA C 13 REMARK 465 DA C 14 REMARK 465 DC C 15 REMARK 465 GLY A 91 REMARK 465 GLU A 92 REMARK 465 ASP A 93 REMARK 465 ARG A 94 REMARK 465 ARG A 95 REMARK 465 VAL A 96 REMARK 465 PRO A 97 REMARK 465 GLN A 98 REMARK 465 PRO A 112 REMARK 465 ASN A 113 REMARK 465 ALA A 114 REMARK 465 SER A 115 REMARK 465 ASP A 116 REMARK 465 PRO A 117 REMARK 465 SER A 118 REMARK 465 GLU A 191 REMARK 465 THR A 192 REMARK 465 LEU A 193 REMARK 465 LYS A 194 REMARK 465 GLU A 195 REMARK 465 ARG A 196 REMARK 465 ASP A 197 REMARK 465 GLU A 198 REMARK 465 ILE A 337 REMARK 465 GLN A 338 REMARK 465 LYS A 339 REMARK 465 PRO A 340 REMARK 465 GLU A 341 REMARK 465 TYR A 342 REMARK 465 SER A 343 REMARK 465 GLU A 344 REMARK 465 GLY B 91 REMARK 465 GLU B 92 REMARK 465 ASP B 93 REMARK 465 ARG B 94 REMARK 465 ARG B 95 REMARK 465 VAL B 96 REMARK 465 PRO B 97 REMARK 465 GLN B 98 REMARK 465 PRO B 112 REMARK 465 ASN B 113 REMARK 465 ALA B 114 REMARK 465 SER B 115 REMARK 465 ASP B 116 REMARK 465 PRO B 117 REMARK 465 SER B 118 REMARK 465 GLU B 191 REMARK 465 THR B 192 REMARK 465 LEU B 193 REMARK 465 LYS B 194 REMARK 465 GLU B 195 REMARK 465 ARG B 196 REMARK 465 ASP B 197 REMARK 465 GLU B 198 REMARK 465 ILE B 337 REMARK 465 GLN B 338 REMARK 465 LYS B 339 REMARK 465 PRO B 340 REMARK 465 GLU B 341 REMARK 465 TYR B 342 REMARK 465 SER B 343 REMARK 465 GLU B 344 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 DA E 10 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DA E 10 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA E 10 C2 N3 C4 REMARK 470 DA C 10 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DA C 10 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA C 10 C2 N3 C4 REMARK 470 ASN A 99 CG OD1 ND2 REMARK 470 GLU A 107 CG CD OE1 OE2 REMARK 470 ASP A 110 CG OD1 OD2 REMARK 470 LYS A 111 CD CE NZ REMARK 470 VAL A 119 CG1 CG2 REMARK 470 ASN A 128 CG OD1 ND2 REMARK 470 ARG A 135 CZ NH1 NH2 REMARK 470 LYS A 143 CG CD CE NZ REMARK 470 GLN A 144 CG CD OE1 NE2 REMARK 470 GLN A 190 CG CD OE1 NE2 REMARK 470 ASN A 199 CG OD1 ND2 REMARK 470 LYS A 202 CG CD CE NZ REMARK 470 HIS A 211 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 229 CG CD OE1 OE2 REMARK 470 LYS A 299 CG CD CE NZ REMARK 470 GLN A 335 CG CD OE1 NE2 REMARK 470 ASN A 336 CG OD1 ND2 REMARK 470 GLU B 107 CG CD OE1 OE2 REMARK 470 ASP B 110 CG OD1 OD2 REMARK 470 LYS B 111 CD CE NZ REMARK 470 VAL B 119 CG1 CG2 REMARK 470 ASN B 128 CG OD1 ND2 REMARK 470 LYS B 143 CG CD CE NZ REMARK 470 GLN B 144 CG CD OE1 NE2 REMARK 470 GLN B 190 CG CD OE1 NE2 REMARK 470 ASN B 199 CG OD1 ND2 REMARK 470 LYS B 202 CG CD CE NZ REMARK 470 HIS B 211 CG ND1 CD2 CE1 NE2 REMARK 470 GLU B 229 CG CD OE1 OE2 REMARK 470 LYS B 299 CG CD CE NZ REMARK 470 GLN B 335 CG CD OE1 NE2 REMARK 470 ASN B 336 CG OD1 ND2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE2 GLU A 167 O HOH A 501 1.94 REMARK 500 O GLN B 263 O HOH B 401 2.06 REMARK 500 O HOH B 403 O HOH B 458 2.07 REMARK 500 O HOH B 577 O HOH B 615 2.07 REMARK 500 OD1 ASN B 232 O HOH B 402 2.11 REMARK 500 O GLN A 263 O HOH A 502 2.12 REMARK 500 O HOH A 503 O HOH A 665 2.12 REMARK 500 O HOH B 576 O HOH B 613 2.12 REMARK 500 O HOH E 117 O HOH A 647 2.13 REMARK 500 O LEU B 200 O HOH B 403 2.13 REMARK 500 O HOH A 728 O HOH A 739 2.14 REMARK 500 O HOH C 102 O HOH C 103 2.16 REMARK 500 O HOH C 120 O HOH B 583 2.16 REMARK 500 O HOH A 515 O HOH A 600 2.16 REMARK 500 O5' DA C 10 O HOH C 101 2.17 REMARK 500 O HOH A 678 O HOH A 680 2.17 REMARK 500 O HOH E 121 O HOH E 124 2.17 REMARK 500 O HOH B 558 O HOH B 575 2.18 REMARK 500 O HOH A 532 O HOH A 662 2.18 REMARK 500 O HOH B 452 O HOH B 588 2.19 REMARK 500 O HOH B 435 O HOH B 543 2.19 REMARK 500 O HOH A 643 O HOH A 687 2.19 REMARK 500 O HOH B 491 O HOH B 585 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 628 O HOH B 411 2564 2.10 REMARK 500 O HOH A 560 O HOH A 721 3345 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DA E 4 P DA E 4 O5' 0.071 REMARK 500 DA E 4 C5' DA E 4 C4' 0.048 REMARK 500 DA C 4 P DA C 4 O5' 0.074 REMARK 500 DA C 4 C5' DA C 4 C4' 0.050 REMARK 500 CYS A 239 CB CYS A 239 SG -0.108 REMARK 500 CYS B 239 CB CYS B 239 SG -0.114 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS A 239 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG B 135 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 CYS A 239 136.55 -170.66 REMARK 500 PHE A 266 -125.90 55.17 REMARK 500 CYS B 239 136.95 -170.40 REMARK 500 PHE B 266 -124.16 54.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 741 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH B 622 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH B 623 DISTANCE = 6.11 ANGSTROMS REMARK 525 HOH B 624 DISTANCE = 6.14 ANGSTROMS REMARK 525 HOH B 625 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH B 626 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH B 627 DISTANCE = 7.79 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 401 DBREF 5ZYU E 1 15 PDB 5ZYU 5ZYU 1 15 DBREF 5ZYU C 1 15 PDB 5ZYU 5ZYU 1 15 DBREF 5ZYU A 91 344 UNP Q9BQP7 MGME1_HUMAN 91 344 DBREF 5ZYU B 91 344 UNP Q9BQP7 MGME1_HUMAN 91 344 SEQRES 1 E 15 DA DA DC DA DA DC DA DA DC DA DA DC DA SEQRES 2 E 15 DA DC SEQRES 1 C 15 DA DA DC DA DA DC DA DA DC DA DA DC DA SEQRES 2 C 15 DA DC SEQRES 1 A 254 GLY GLU ASP ARG ARG VAL PRO GLN ASN TRP PHE PRO ILE SEQRES 2 A 254 PHE ASN PRO GLU ARG SER ASP LYS PRO ASN ALA SER ASP SEQRES 3 A 254 PRO SER VAL PRO LEU LYS ILE PRO LEU GLN ARG ASN VAL SEQRES 4 A 254 ILE PRO SER VAL THR ARG VAL LEU GLN GLN THR MET THR SEQRES 5 A 254 LYS GLN GLN VAL PHE LEU LEU GLU ARG TRP LYS GLN ARG SEQRES 6 A 254 MET ILE LEU GLU LEU GLY GLU ASP GLY PHE LYS GLU TYR SEQRES 7 A 254 THR SER ASN VAL PHE LEU GLN GLY LYS ARG PHE HIS GLU SEQRES 8 A 254 ALA LEU GLU SER ILE LEU SER PRO GLN GLU THR LEU LYS SEQRES 9 A 254 GLU ARG ASP GLU ASN LEU LEU LYS SER GLY TYR ILE GLU SEQRES 10 A 254 SER VAL GLN HIS ILE LEU LYS ASP VAL SER GLY VAL ARG SEQRES 11 A 254 ALA LEU GLU SER ALA VAL GLN HIS GLU THR LEU ASN TYR SEQRES 12 A 254 ILE GLY LEU LEU ASP CYS VAL ALA GLU TYR GLN GLY LYS SEQRES 13 A 254 LEU CYS VAL ILE ASP TRP LYS THR SER GLU LYS PRO LYS SEQRES 14 A 254 PRO PHE ILE GLN SER THR PHE ASP ASN PRO LEU GLN VAL SEQRES 15 A 254 VAL ALA TYR MET GLY ALA MET ASN HIS ASP THR ASN TYR SEQRES 16 A 254 SER PHE GLN VAL GLN CYS GLY LEU ILE VAL VAL ALA TYR SEQRES 17 A 254 LYS ASP GLY SER PRO ALA HIS PRO HIS PHE MET ASP ALA SEQRES 18 A 254 GLU LEU CYS SER GLN TYR TRP THR LYS TRP LEU LEU ARG SEQRES 19 A 254 LEU GLU GLU TYR THR GLU LYS LYS LYS ASN GLN ASN ILE SEQRES 20 A 254 GLN LYS PRO GLU TYR SER GLU SEQRES 1 B 254 GLY GLU ASP ARG ARG VAL PRO GLN ASN TRP PHE PRO ILE SEQRES 2 B 254 PHE ASN PRO GLU ARG SER ASP LYS PRO ASN ALA SER ASP SEQRES 3 B 254 PRO SER VAL PRO LEU LYS ILE PRO LEU GLN ARG ASN VAL SEQRES 4 B 254 ILE PRO SER VAL THR ARG VAL LEU GLN GLN THR MET THR SEQRES 5 B 254 LYS GLN GLN VAL PHE LEU LEU GLU ARG TRP LYS GLN ARG SEQRES 6 B 254 MET ILE LEU GLU LEU GLY GLU ASP GLY PHE LYS GLU TYR SEQRES 7 B 254 THR SER ASN VAL PHE LEU GLN GLY LYS ARG PHE HIS GLU SEQRES 8 B 254 ALA LEU GLU SER ILE LEU SER PRO GLN GLU THR LEU LYS SEQRES 9 B 254 GLU ARG ASP GLU ASN LEU LEU LYS SER GLY TYR ILE GLU SEQRES 10 B 254 SER VAL GLN HIS ILE LEU LYS ASP VAL SER GLY VAL ARG SEQRES 11 B 254 ALA LEU GLU SER ALA VAL GLN HIS GLU THR LEU ASN TYR SEQRES 12 B 254 ILE GLY LEU LEU ASP CYS VAL ALA GLU TYR GLN GLY LYS SEQRES 13 B 254 LEU CYS VAL ILE ASP TRP LYS THR SER GLU LYS PRO LYS SEQRES 14 B 254 PRO PHE ILE GLN SER THR PHE ASP ASN PRO LEU GLN VAL SEQRES 15 B 254 VAL ALA TYR MET GLY ALA MET ASN HIS ASP THR ASN TYR SEQRES 16 B 254 SER PHE GLN VAL GLN CYS GLY LEU ILE VAL VAL ALA TYR SEQRES 17 B 254 LYS ASP GLY SER PRO ALA HIS PRO HIS PHE MET ASP ALA SEQRES 18 B 254 GLU LEU CYS SER GLN TYR TRP THR LYS TRP LEU LEU ARG SEQRES 19 B 254 LEU GLU GLU TYR THR GLU LYS LYS LYS ASN GLN ASN ILE SEQRES 20 B 254 GLN LYS PRO GLU TYR SER GLU HET GOL A 401 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *532(H2 O) HELIX 1 AA1 LEU A 125 ILE A 130 1 6 HELIX 2 AA2 SER A 132 GLN A 139 1 8 HELIX 3 AA3 THR A 142 GLY A 161 1 20 HELIX 4 AA4 GLY A 161 SER A 188 1 28 HELIX 5 AA5 ASN A 199 LYS A 202 5 4 HELIX 6 AA6 SER A 203 VAL A 209 1 7 HELIX 7 AA7 VAL A 209 LYS A 214 1 6 HELIX 8 AA8 PHE A 261 PHE A 266 5 6 HELIX 9 AA9 ASP A 267 HIS A 281 1 15 HELIX 10 AB1 ASP A 310 ASN A 334 1 25 HELIX 11 AB2 LEU B 125 ILE B 130 1 6 HELIX 12 AB3 SER B 132 GLN B 139 1 8 HELIX 13 AB4 THR B 142 GLY B 161 1 20 HELIX 14 AB5 GLY B 161 SER B 188 1 28 HELIX 15 AB6 ASN B 199 LYS B 202 5 4 HELIX 16 AB7 SER B 203 VAL B 209 1 7 HELIX 17 AB8 VAL B 209 LYS B 214 1 6 HELIX 18 AB9 PHE B 261 PHE B 266 5 6 HELIX 19 AC1 ASP B 267 HIS B 281 1 15 HELIX 20 AC2 ASP B 310 ASN B 334 1 25 SHEET 1 AA1 5 VAL A 216 HIS A 228 0 SHEET 2 AA1 5 TYR A 233 TYR A 243 -1 O GLU A 242 N SER A 217 SHEET 3 AA1 5 LYS A 246 THR A 254 -1 O CYS A 248 N ALA A 241 SHEET 4 AA1 5 CYS A 291 ALA A 297 1 O ALA A 297 N LYS A 253 SHEET 5 AA1 5 HIS A 305 MET A 309 -1 O MET A 309 N GLY A 292 SHEET 1 AA2 5 VAL B 216 HIS B 228 0 SHEET 2 AA2 5 TYR B 233 TYR B 243 -1 O VAL B 240 N ARG B 220 SHEET 3 AA2 5 LYS B 246 THR B 254 -1 O CYS B 248 N ALA B 241 SHEET 4 AA2 5 CYS B 291 ALA B 297 1 O VAL B 295 N LYS B 253 SHEET 5 AA2 5 HIS B 305 MET B 309 -1 O HIS B 307 N ILE B 294 SITE 1 AC1 6 PHE A 266 ASP A 267 LYS A 320 HOH A 506 SITE 2 AC1 6 HOH A 518 HOH A 541 CRYST1 80.714 80.714 79.769 90.00 90.00 120.00 P 32 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.012389 0.007153 0.000000 0.00000 SCALE2 0.000000 0.014306 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012536 0.00000